LW-FQZip2

Experimental studies

LW-FQZip 2 is compared with other state-of-the-art FASTQ data compression algorithms (including Quip, DSRC2, CRAM, FQZcomp, LFQC, LEON, SCALCE, LW-FQZip 1, bzip2, and gzip) using 10 real-world FASTQ files download from the Sequence Read Archive of the National Centre for Biotechnology Information (NCBI). The experimental results demonstrate that LW-FQZip 2 obtains superior compression ratios to other methods at reasonalbe time and memory costs. More discussions are available in our paper. The details of implementation, data sets, and experimental studies are provided in the supplementary file.

Table 1: Compression results of LW-FQZip 2 ( Normal mode )

	Dataset	Platform	Size(MB)	Compressed ratio	Compressed size(MB)	Compressed time(S)	Decompressed time(S)
Long-read	SRR2916693	454 GS	425	16.5%	71	35	25
	SRR2994368	Illumina Miseq	4688	17.3%	812	300	240
	SRR3211986	Pacbio RS	1759	33.3%	585	203	400
	ERR739513	MinION	871	35.2%	307	122	170
	SRR3190692	Illumina MiSeq	11379	12.7%	1441	540	416

short-read	ERR385912	Illumina Hiseq 2000	641	6.4%	41	25	12
	ERR386131	Ion Torrent PGM	1371	16.5%	226	87	73
	SRR034509	Illumina Analyzer II	5247	23.7%	1241	301	275
	ERR174310	Illumina Hiseq 2000	105122	21.0%	22061	14050	10428
	ERR194147	Illumina Hiseq 2000	202631	20.1%	40812	26488	19737

Table 2: Compression results of LW-FQZip 2(-g) ( High compression ratio mode )

	Dataset	Platform	Size(MB)	Compressed ratio	Compressed size(MB)	Compressed time(S)	Decompressed time(S)
Long-read	SRR2916693	454 GS	425	15.3%	65	303	295
	SRR2994368	Illumina Miseq	4688	16.0%	748	1260	1198
	SRR3211986	Pacbio RS	1759	32.3%	568	759	725
	ERR739513	MinION	871	34.8%	303	333	320
	SRR3190692	Illumina MiSeq	11379	11.7%	1330	2520	2372

short-read	ERR385912	Illumina Hiseq 2000	641	5.0%	32	282	268
	ERR386131	Ion Torrent PGM	1371	16.0%	219	324	301
	SRR034509	Illumina Analyzer II	5247	22.7%	1193	1200	1080
	ERR174310	Illumina Hiseq 2000	105122	20.1%	21152	42600	30000
	ERR194147	Illumina Hiseq 2000	202631	14.3%	28915	71400	60540

Compression ratio (all methods are configured to obtain the best compression ratios)

Note: 0 means that unknown errors occur in the compression